I think I'm about to recommend the same approach as Askyn. Please forgive any duplication.
I owned 2 different Sony Readers before joining the Nook family with a NST and, later, a Nook Tablet. I ended up returning a Sony T1 before making the switch to Nook because I was fed up with the bugs and general lack of support from Sony (IMHO, anyway). However, the one redeeming quality of the Sony line was the flexibility to manage collections on the Reader with Calibre's use of tags.
The Nook shelving process is atrocious. Frankly, I'm surprised that B&N seems to have ignored the consistent feedback on that for so long. What does work for me, though, is Calibre's excellent ability to create a catalog of my library. If you haven't explored this feature of Calibre, you should. It's worth your time.
The catalog can be customized to your liking. I have my catalog indexed to show books by title, author, and series. (Series really being the most important to me.) If I'm trying to remember what's next on my reading list or deciding what to pick up next, I simply open the catalog on my device and browse. While I still have to go back to the device's library to select the book once I've made my decision, I think it's still a much better option than filling Nook shelves book by book.
This has worked well for me- hope it helps!
tl;dr Create a catalog in Calibre and sideload that on your device
Last edited by MooseFam5; 12-30-2012 at 09:28 AM.
Reason: fixing a typo! clearly, not enough coffee yet this morning